Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP63

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
ΔNp63α-expressing HepG2 cells
cell type
HepG2 cells
passages
10-12
chip antibody
HA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated cell pellets, ΔNp63-DNA and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). After adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq??? following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
14796907
Reads aligned (%)
98.7
Duplicates removed (%)
10.7
Number of peaks
841 (qval < 1E-05)

hg19

Number of total reads
14796907
Reads aligned (%)
97.8
Duplicates removed (%)
11.5
Number of peaks
946 (qval < 1E-05)

Base call quality data from DBCLS SRA